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Update usage.md

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@ -230,7 +230,7 @@ You can optionally save the FASTQ output of the run merging with the `--save_run
###### MALT
nf-core/taxprofiler uses MALT 0.4.1, which is a compatively old version. However it has been found that the most recent version of MALT (0.5.\*), at the time of writing, is broken. [The the LCA step appears not to be executed](http://megan.informatik.uni-tuebingen.de/t/lca-placement-failure-with-malt-v-0-5-2-and-0-5-3/1996/3), pushing all hits to the leaves of the taxonomy. However, if you need to use a more recent taxonomy map file with your databases, the output of `malt-build` from MALT 0.5.3 should be still be compatible with `malt-run` of 0.4.1.
nf-core/taxprofiler uses MALT 0.4.1, which is a compatively old version. However it has been found that the most recent version of MALT (0.5.\*), at the time of writing, is broken. [The LCA step appears not to be executed](http://megan.informatik.uni-tuebingen.de/t/lca-placement-failure-with-malt-v-0-5-2-and-0-5-3/1996/3), pushing all hits to the leaves of the taxonomy. However, if you need to use a more recent taxonomy map file with your databases, the output of `malt-build` from MALT 0.5.3 should be still be compatible with `malt-run` of 0.4.1.
### Updating the pipeline